A good overview of The Chrysalids may be found here. Some themes prevalent in the novel include:

1. Isolation and Alienation: David and the "abberrations" are considered as outcasts and alienated from Waknuk's society.

2. Religious persecution

3. Betrayal

4. Salem on Literature says "The Chrysalids proposes that ignorant adherence to the “word,” or to religious tenets, has dehumanized the world, and that only in transcendence of past beliefs will humanity resurrect itself. The message is distinct: People must throw off the mind-forged chains of the past, bury fears and prejudices, and walk as one with enlightened steps into the future, or else stumble and perish forever."

A few other themes in The Chrysalids are Power vs. powerlessness, Hope & Change.

Power vs. Powerlessness

>Can be seen through David and Joseph when Joseph reprimanded David for wishing fora third hand. David "stumbled and stuttered" and was "alarmed, and too confused" to say anything. Joseph treated David in a harsh manner for such a petty reason, and David did not retaliate, which shows that he was powerless against his father.

>Another scenario was when Aunt Harriet went to the Strorm household to seek help from Emily. There, she was turned down by Joseph and Emily, and Aunt Harriet accepted defeat because she turned to go, out of hope. We can see that she is powerless as compared to Joseph and Emily.

Hope & Change

>The telepaths are mediums of change in the rigid, narrow-minded and inflexible society of Waknuk. They are out of the ordinary and are evolved, new types of human beings.

>Petra brings hope to the telepaths due to her extremely strong powers of telepathy. Her difference also brings out the topic of change.

>The Sealand woman is an advocate for change because she thinks "change is essential". She believes that the human race should not condemn change but should welcome it whole-hearted because only with change can a society progress.

The people of Waknuk believe that Deviants are an abomination and the work of the Devil. From a young age, the Definition of Man and the importance of Purity are drilled into them. This causes them to have a fixed mindset to persecute Deviants when they grow up. It can also be seen from how they regularly undergo inspections to destroy all Deviations from their property, like in the case of the Strorm household, especially Joseph, who take it as a personal insult to have a deviated crop or livestock in their farm. Deviant humans are cruelly sterilized and abandoned in the Fringes, never allowed to return. This harsh treatment of Deviations shows us that Waknuk is intolerant of and prejudiced against Deviation.

Conformity to the Norm

Waknuk as a society have this all-consuming passion for conformity. Offences are either burnt or mercilessly slaughtered, Blasphemies were banished, and women who had given birth to deformed babies three times were ostracised and kicked out of their homes. They believed in nothing else but the True Image, and nobody was allowed to think differently.

Oppression

‘Blasphemies’ are sterilized because of the oppressive Waknuk laws and thrust naked by the oppressive authorities into the Fringes, alone and vulnerable, without ever a say for themselves. In defiance of the excessive oppression present in Waknuk that would even condemn her innocent little baby, Aunt Harriet killed herself. David suffered terribly under the oppression of his own father, who punished him brutally and kept him in check with the threat of often unjust force and authority.

Purity and the definition of Man

Being the only safe ‘haven’ amongst unchecked Deviation in the Fringes and beyond, the people of Waknuk are constantly afraid that they will be overrun by these Deviations which they perceive as intolerable evil and the Devil’s work. Knowing no better, they turned to their Purity laws to protect themselves, and the extent of their fears has caused them to become obsessive about maintaining these laws to the extent of harming innocent children who were unfortunately born with defects.

Static vs. Change

Waknuk did not want to change anything about their society, and wanted to keep ferreting out Deviations until the whole society was pure and true according to the standards of their so-called faith. As a result of their rigidity, they became a stagnant society because there was no progress forward. However, in the conflict between the Waknuk citizens, Fringes people and Sealand people, it is the natives who die.

“The essential quality of life is living; the essential quality of living is change; change is evolution: and we are part of it. The static, the enemy of change, is the enemy of life, and therefore our implacable enemy”.

From the Sealand woman's argument, we see they are superior to the people of Waknuk, because they accepted change, whereas Waknuk did all they can to stop it. In the end, the Waknuk people, including Joseph, died and the Sealand people won. This represents the struggle of static vs. change.